diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch | 80 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/dialign-tx/package.py | 2 |
2 files changed, 82 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch b/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch new file mode 100644 index 0000000000..5a82f97e7b --- /dev/null +++ b/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch @@ -0,0 +1,80 @@ +--- a/source/alig.c 2008-12-06 04:10:05.000000000 -0800 ++++ b/source/alig.c 2017-11-21 10:58:31.000000000 -0800 +@@ -520,7 +520,7 @@ + * datastructure (i.e. frontiers). The given diag must be consistent + * to the given alignment ! + */ +-inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { ++char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { + + char alignedSomething = 0; + int i,j,k; +diff -Naur a/source/assemble.c b/source/assemble.c +--- a/source/assemble.c 2008-12-06 04:10:05.000000000 -0800 ++++ b/source/assemble.c 2017-11-21 10:57:55.000000000 -0800 +@@ -10,7 +10,7 @@ + + extern void error(char *message); + extern void merror(char *msg1, char *msg2); +-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ++extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + struct prob_dist *pdist); + extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + struct prob_dist *pdist); +@@ -37,7 +37,7 @@ + extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); + extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc); + //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); +-extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ++extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); + //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand); + //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg); + +@@ -574,7 +574,7 @@ + * returns a value <0 if there is an non-conflicting overlap + * returns 0 in all other non-conflicting cases + */ +-inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { ++static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { + // if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!"); + int s1_1 = dg1->seq_p1.num; + int s1_2 = dg1->seq_p2.num; +diff -Naur a/source/diag.c b/source/diag.c +--- a/source/diag.c 2008-12-06 04:10:05.000000000 -0800 ++++ b/source/diag.c 2017-11-21 10:55:43.000000000 -0800 +@@ -183,7 +183,7 @@ + * omitScore = 0: normal + * omitScore = 1: no score calculation + */ +-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix, ++static inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix, + struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { + + if(dg->multi_dg) { +@@ -302,7 +302,7 @@ + } + } + +-inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ++void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + struct prob_dist *pdist) { + real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); + } +@@ -312,7 +312,7 @@ + /** + * calculates the overlap weight for the given diag + */ +-inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ++static inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + struct prob_dist *pdist) { + int sn1 = dg->seq_p1.num; + int sn2 = dg->seq_p2.num; +@@ -958,7 +958,7 @@ + * The pointer returned (and the ones included in the struct) + * has to be deallocted explicitely from memory. + */ +-inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, ++static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, + struct prob_dist *pdist, struct seq* seq1, + struct seq* seq2, struct alignment *algn, + long double **tmp_dist, int round) { diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py index 009793216f..182069a013 100644 --- a/var/spack/repos/builtin/packages/dialign-tx/package.py +++ b/var/spack/repos/builtin/packages/dialign-tx/package.py @@ -50,3 +50,5 @@ class DialignTx(MakefilePackage): install('dialign-tx', prefix.bin) # t-coffee recognizes as dialign-t install('dialign-tx', join_path(prefix.bin, 'dialign-t')) + + patch('dialign-1-0-2-gcc-5-4-0.patch', when='%gcc@5.4.0') |